Thursday, May 12, 2016

A Response to VJ Torley

One Long Argument

To read VJ Torley’s analysis of my criticism of S. Joshua Swamidass’ recent article, Evidence and Evolution, one would think that I mercilessly berated a poor fellow who was merely attempting to “extend an olive branch to creationists.” After all, nowhere did Swamidass belittle or ridicule his opponents, and nowhere was there so much as a trace of the smug superiority. And the guy is a Christian, not some atheistic reductionist. In fact, Swamidass does not even draw any conclusions in his article.

This is how Torley begins his article and unfortunately this gives those who have not read the two articles the wrong impression. I gave a lengthy, fact-based, scientific criticism of Swamidass’ claims which was not dismissive or sarcastic. I did not accuse of Swamidass of belittling or ridiculing anyone, nor did I accuse him of smugness, academic or otherwise. And I did not question his religious beliefs. All of this was injected by Torley.

As for drawing conclusions, yes contrary to Torley, Swamidass draws conclusions. He states in no uncertain terms that the evolutionary story “is by far the best scientific explanation of our origins.” In fact, the evidence is stunning:

What is the evidence for human common ancestry with apes? The strongest evidence is a series of stunningly accurate predictions about human genomes that have been confirmed in recent decades as the human and ape genomes have been sequenced.

The idea that Swamidass does not draw conclusions is inaccurate. Swamidass goes on to suggest that microevolution is sufficient to explain the evolution of humans from a small, ape-like creature.

Throughout his piece, Swamidass uses a scientist versus theologian, Warfare Thesis perspective. Scientists simply refer to the data whereas theologians must adjust their sights, drop their denial, and grapple with the undeniable truths of evolution. To object is futile and attempts to explain humans as a product of design are “lawyerly”:

A common lawyerly objection to this evidence is that these similarities are “equally” explained by common “design.” As scientists, our response to this objection is data.

Perhaps the theologian “could look for errors in the scientific analyses,” but even that would be futile:

Still, even if he [the theologian] found standing for quibbles here and there, the overall picture would remain the same and the evidence against common ancestry, at best, would be subtle and debatable.

Swamidass presents a story in order to “reduce the fear some feel when encountering evidence that might contradict their understanding of the Bible.”

This is all Warfare Thesis, and Torley finds it to be “irenic in tone, easy to follow, deeply learned, and absolutely right.”

On the other hand Torley throws occasional ad hominems my way and finds that my critique of Swamidass’ piece was “polemical and curtly dismissive in tone.” In fact, my criticism was about Swamidass’ arguments. I pointed out that his scientific claims were erroneous and that ultimately his arguments relied on metaphysical claims.

This is not to say there cannot be improvements in my article. It is, after all, a blog post. I’m thankful for feedback and corrections to my errors. But Torley’s casting of the two articles is simply a misrepresentation. It seems that his criticism of my post is, in fact, more applicable to his article.What about the science?

Torley next castigates me for ignoring the main scientific evidence Swamidass presents. And what is Torley referring to? A series of references Swamidass made. So instead of addressing the key scientific claims made by Swamidass (which I did), I am supposed to do an expansive analysis on several references Swamidass provided as backup.

In fact I was planning on getting to those references at some point, time permitting, as they are yet more examples of failed science. But Torley’s requirements and criticisms are unrealistic.

Torley next quotes from one of Swamidass’ references, imagines what my response would be, and argues with it. This is getting silly. Normally I would not respond to this type of article, but this is different since it appears so close to my article.

Torley finishes with a series of erroneous rebuttals, ad hominems, and strawmen arguments. To be sure, Torley makes some good tangential points, but they are unfortunately the minority in a series of failed arguments.

Not surprisingly Torley shares Swamidass’ theological convictions which underwrite their claims. Their contrastive reasoning, if correct, proves their case. As Torley writes:

On a special creationist account of human origins, there is absolutely no reason to expect that humans would have what appear to be the remains of genes used for making egg yolks in their DNA – just as there is no particular reason to expect that humans would be more genetically similar to chimps than rats are to mice – or for that matter, than foxes are to wolves, or horses are to donkeys. [emphasis in original]

No reason. If Torley is correct here then, yes, we can safely conclude for evolution. Likewise:

Reasoning on Bayesian grounds, these striking and singular facts have a high probability on the hypothesis of common descent, but are surprising (and hence improbable) on a hypothesis of separate creation. One can only conclude that these facts lend scientific support to the hypothesis of common descent.

True enough. Such reasoning is perfectly valid, but it hinges on metaphysical premises. From a scientific perspective, evolution and common descent are unlikely to say the least, but from a metaphysical perspective, they are compelling.

Actually, you could say that experiment has already been done. Placental mammals have all 3 vitellogenin genes knocked out. They produce no proteins and there is no vitellogenin in their eggs. Monotremes such as the platypus still have one functional gene.

Just because they're kept in ovaries and attached to a uterus instead of being laid doesn't mean there's no yolk. According to what I read, there is a minute amount of ooplasm, aka egg yolk, in a human egg.

How do we explain the genome similarities between humans and chimpanzees?Before we make an attempt to answer this question, one thing should be perfectly clear: the similarities between genomes cannot be explained by a process that cannot explain any genome.

Here is an excerpt from a post of mine that I do not hold to BUT that is an evolutionary atheist position taken based on the same evidence as the neo-Darwinian story:========================...A few people likewise believe that apes (Gorillas) are descended from mankind in some way. For instance, Dr. Aaron G. Filler:

✦ Dr. Aaron G. Filler, M.D., Ph.D. studied evolutionary theory under some of the leading biologists and anthropologists of our time: Ernst Mayr, Stephen J. Gould, David Pilbeam, and Irven DeVore. A neurosurgeon at the Institute for Spinal Disorders at Cedars Sinai Medical Center and past associate director of the Comprehensive Spine Center at UCLA, Dr. Filler has been a leading innovator in medical imaging and neuroscience. He is the author of Do You Really Need Back Surgery? (Oxford University Press), as well as numerous scientific articles and patents.

He wrote a book entitled The Upright Ape: A New Origin of the Species, in which he follows the footsteps of another well respected scientist showing that apes are most likely a breakaway group from mankind. The other scientist I mention is Dr. Geoffrey H. Bourne:

✦ He was Director of Yerkes Regional Primate Research Center at Emory University, England. Dr. Bourne is Oxford educated, and is an American cell biologist/anatomist who was considered by most to be the worlds leading primatologist.

He said that apes are descended from man. Why would men of science believe such a thing? Because science has never seen any information being added to the evolutionary upward “slant” that is required by its theory (Darwinism, e.g., “scientism”). So since apes are less than us, Dr. Bourne says that science [not “scientism”] proves his theory due to observable facts. ...

Given recombination there is no way to know how similar two (allegedly) diverged genomes would be after hundreds of thousands of generations.

And given how allegedly similar chimps and human genomes are it should be easy to map the transformations required to the genetics. Yet no one has come close.

As for a common design DEnnis Venema sez that the two genomes are too similar than what they need to be. How he knows what they need to be is beyond me. How he knows what descent with modification will do over hundreds of thousands of generations is also beyond me.

"On a special creationist account of human origins, there is absolutely no reason to expect that humans would have what appear to be the remains of genes used for making egg yolks in their DNA – just as there is no particular reason to expect that humans would be more genetically similar to chimps than rats are to mice – or for that matter, than foxes are to wolves, or horses are to donkeys. "

I don't know what ID can make of that. If you guys out here, ID specialists, could explain why humans and chimps are more closely related to each other than mouses to rats that would be nice.

But I'm sure you won't even try and just spew nonsense about how evolutionary biology has no clue either.

CalamityI don't know what ID can make of that. If you guys out here, ID specialists, could explain why humans and chimps are more closely related to each other than mouses to rats that would be nice.If you look at the abstract below you will see splicing differences among vertebrates. Splicing is the final step before MRNA becomes a protein. It can dramatically effect the function of the protein so the bottom line is DNA only tells part of the story. The largest difference in alternative splicing between vertebras is the difference between chimps and man with man having 70 to 90% of mRNA spliced and chimps half that numberAll Science JournalsADVANCEDEnter Search Term￼￼￼￼￼￼￼My ScienceAbout the JournalPrev | Table of Contents | Next Read Full Text to Comment (0)￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼The Evolutionary Landscape of Alternative Splicing in Vertebrate SpeciesNuno L. Barbosa-Morais1,2, Manuel Irimia1,*, Qun Pan1,*, Hui Y. Xiong3,*, Serge Gueroussov1,4,*,Leo J. Lee3, Valentina Slobodeniuc1, Claudia Kutter5, Stephen Watt5, Recep Çolak1,6, TaeHyung Kim1,7, Christine M. Misquitta-Ali1, Michael D. Wilson4,5,7, Philip M. Kim1,4,6, Duncan T. Odom5,8,Brendan J. Frey1,3, Benjamin J. Blencowe1,4,†Author Affiliation￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼ABSTRACTHow species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species- specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.Science 21 December 2012:Vol. 338 no. 6114 pp. 1587-1593 DOI: 10.1126/science.1230612RESEARCH ARTICLEAll Science JournalsADVANCEDEnter Search Term￼￼￼￼￼￼￼My ScienceAbout the JournalPrev | Table of Contents | Next Read Full Text to Comment (0)￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼The Evolutionary Landscape of Alternative Splicing in Vertebrate SpeciesNuno L. Barbosa-Morais1,2, Manuel Irimia1,*, Qun Pan1,*, Hui Y. Xiong3,*, Serge Gueroussov1,4,*,Leo J. Lee3, Valentina Slobodeniuc1, Claudia Kutter5, Stephen Watt5, Recep Çolak1,6, TaeHyung Kim1,7, Christine M. Misquitta-Ali1, Michael D. Wilson4,5,7, Philip M. Kim1,4,6, Duncan T. Odom5,8,Brendan J. Frey1,3, Benjamin J. Blencowe1,4,†Author Affiliations↵†To whom correspondence should be addressed. E-mail: b.blencowe@utoronto.ca ↵* These authors contributed equally to this work.￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼+￼￼￼￼￼￼ABSTRACTHow species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species- specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.

Vincent Torley is a Catholic philosopher who worships medieval Catholic thinkers like Saint Augustine and a few others. Those woefully self-contradictory thinkers introduced a bunch of nonsense into Christian doctrine such as God being omnipotent and omniscient. These are qualities that Yahweh never claimed for himself, especially since they squarely and painfully contradict the concept of free will which Torley pays lip service to. They all came from pagan religions.

The Church of Rome is famous for adopting pagan beliefs and practices. Christmas and Easter are notorious examples. They even managed to insert the pagan concept of everlasting hell into the New Testament Bible, a stupid idea that is never mentioned in the Jewish Old Testament. In addition, they adopted Sunday as the day of rest even though early Christians rested on the Sabbath just like the Jews. Let's not even mention the practice of a celibate priesthood (we don't need no stinking priesthood) that only contributes to attracting homosexuals and pedophiles into the Church.

These facts alone tell me that Torley is out to lunch as a philosopher. He's more like a metaphysician in the tradition of Nostradamus. Torley praises Swamidass because Swamidass uses some of the same erroneous Catholic beliefs in order to make a stupid point about the superiority of science over religion, especially over Christianity. If Swamidass is a Christian, then I am ashamed to be a Christian. He's a weaver of lies and deception in my view.

Swamidass and Torley are two sides of the same religious coin. They exemplify Hunter's point about the warfare mentality of Darwinists and atheists. Darwin's God indeed! Words like mental midgets come to mind.

First day observance was near universal in the east and west from the startThe west was a little funnierPagan festivals were yearly, although such worship was associated with the theater and suchThe gathering and worship day was not kept in a Judaic manner

And can conclude there was no changing of any day of worship by the roman church, and if they claimed to have, there was nothing to have even been changed and taking them at their word is not prudent. The eastern church had more influence than the west to begim with, too. They also claim Peter was the first pope, but he was an apostle, not a bishop. Luther, in the Augsberg Confession in 1530, article 28, makes a clear analysis of this RCC claim too.

This is a little off topic, but seeing as I once held to the particular things you do, and no longer, I ought to make mention. If you disagree, check history.

Indeed the evolution case was defended by the researcher. So we can defend the rejection of this.Anyways its still all comparative analysis.Thats all it is.We look like apes and so we should have ape genes for the looks.It should be a creationist prediction also.Indeed yEC falls into a trap to try to deny our ape body.God made the ape first on creation week.He knew we would look like the ape.In fact i say that was why we do.Its the best animal body FOR a being like ourselves.Its not a coincidence.There is boundaries to biology options. In fact its a blueprint for all creatures to squeeze their KIND identities into.We could not possibly have a better idea.What else could we look like?We alone don't have our own body.Our soul is our unique identity. Our body is decondary.

Hello, a FAQ has been added to my original article that includes a response to Michael Behe's contribution to this conversation. I hope this helps address your questions.http://swami.wustl.edu/evidence-for-evolution

"No reason. If Torley is correct here then, yes, we can safely conclude for evolution. Likewise:"

he actually wrong. the vit gene is a multifunctional gene:

https://www.sciencedaily.com/releases/2011/11/111129092428.htm

"Simply put, the more vitellogenin in bees, the longer they live. Vitellogenin also guides bees to do different social tasks, such caregiving or foraging. It also supports the immune function and is an antioxidant that promotes stress resistance. "

so even if it was functional in the past in the human lineage, it cant be evidence for a commondescent with a yolk producing species.

just last point cornelius (i also poest it the in ud forum): the mice-rat different is also very easy to explain. we know for example that chimp is closer to human then orangutan from genetic prespective. but actually the orangutan is the closer to human from morphological prespective:

cornelius dscccI just posted this on UD. I think splicing plays a big part in this...AbstractThe chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small. The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species. Still, the number of proteins responsible for the phenotypic differences may be smaller since not all genes are directly responsible for phenotypic characters.

dcscccn addition, Schwartz notes, the most cited studies are largely based on the so-called coding region of the genome, which makes up just 2 to 3 percent of an animal's DNA.

Scientists are referring to this tiny part of the genome when they say humans and chimps are so similar, he said.

But other studies that focus on non-coding regions also consistently support a human-chimp link, counters Carel van Schaik of the Anthropological Institute and Museum at the University of Zurich, Switzerland."

IMHO the contradictions are coming from the fact the DNA alone is only a piece of the genetic story (splicing and timing must be included) and this is why the analysis that Cornelius is critiquing is almost certainly wrong.

"Hi Nic. Is Cornelius putting everyone's comments into moderation, or just a select few like myself and others who oppose his views?"

My last comment brought up that message so I would assume it applies to everyone. Hopefully it is the first step in reigning in some of the childish rants spewed by certain individuals.

"The ID side?

Do I win?"

Not even close, my friend. ID and creationism do not even remotely have the ability to censor the evolutionary side of this debate in the public forum. Censorship of opposing views is overwhelmingly the practice of evolutionary thinking.

Not even close, my friend. ID and creationism do not even remotely have the ability to censor the evolutionary side of this debate in the public forum. Censorship of opposing views is overwhelmingly the practice of evolutionary thinking.

Scientific ideas aren't vetted via debate in a public forum Nic. Scientific ideas are vetted based on the quality of their positive evidence published in the professional scientific literature. That's the only thing which determines acceptance or rejection by the scientific community.

Please provide a list of papers ID-Creationists have submitted to such professional journals which were rejected solely because of their pro-ID-Creationist position.

BTW if you want to see an example of censorship look no further that Uncommon Descent, the flagship ID website, which has banned dozens of pro-evolution posters in the last few years.

I wasn't referring to the vetting of ideas, I was referring to the suppression of ideas, not the same thing.

"BTW if you want to see an example of censorship look no further that Uncommon Descent, the flagship ID website, which has banned dozens of pro-evolution posters in the last few years."

I spend next to no time on that blog so I really cannot comment, However, if they are blocking posters simply based on their comments, that is not acceptable. If, however, they are blocking them because they act like Louis Savain, then more power to them.

"I spend next to no time on that blog so I really cannot comment, However, if they are blocking posters simply based on their comments, that is not acceptable. If, however, they are blocking them because they act like Louis Savain, then more power to them."

They block any poster who disagrees with Gordon (KairosFocus) Mullings. I have been banned three times in the last few weeks for that unforgivable sin. Just check out WHM and KF's recent OPs for the comments by Indian Effigy, Ziggy Lorenc and Inquisitor.